[gmx-users] Helix - Ligand binding - mimic stability

Steven Neumann s.neumann08 at gmail.com
Tue Mar 6 16:05:12 CET 2012

Dear Gmx Users,

I am wondering your approach for such system:

Ligand binding alpha helix which is a part of big helical bundle - in
reality the conformation is rather stable. I want to use position
restrained dynamics - surely for terminal residues and possibly for the
residue in the middle? (the lenght is app 9 nm). I want to avoid folding.
What is your opinion?
I want to perform this simulation as a starting point for binding free
energy simulations via Umbrella Sampling then. I will
have experimental validation via ITC.

Please, let me know your opinion.

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